Table 7 MAGENTA pathway analysis on tonsillectomy GWAS

From: Genome-wide association and HLA region fine-mapping studies identify susceptibility loci for multiple common infections

Pathway

Pathway P value

Pathway FDR

Gene

Gene P value

SNP

SNP P value

Intestinal immune network for IgA production

2.00E-06

3.50E-03

LTBR

0.00E + 00

rs10849448

2.35E-35

   

TNFSF13B

0.00E + 00

rs200748895

1.20E-17

   

TNFRSF13B

0.00E + 00

rs34557412

2.66E-21

   

CD40

3.19E-10

rs6032664

7.31E-12

   

ICOS

1.40E-03

rs231779

1.52E-06

   

CXCR4

4.75E-03

rs2680880

6.91E-06

   

CCL27

7.23E-03

rs12350154

6.71E-06

   

TNFRSF17

8.69E-03

rs456178

1.13E-05

   

IL6

9.25E-03

rs57561814

7.45E-06

   

IL15RA

1.63E-02

rs11256464

6.99E-06

TACI and BCMA stimulation of B-cell immune responses.

9.00E-04

7.80E-03

TNFSF13B

0.00E + 00

rs200748895

1.20E-17

   

TNFRSF13B

0.00E + 00

rs34557412

2.66E-21

   

NFKB1

9.08E-14

rs230523

4.54E-14

   

TNFRSF17

8.69E-03

rs456178

1.13E-05

   

TRAF2

1.21E-02

rs17250694

1.56E-05

Ceramide signaling pathway

3.00E-04

7.95E-03

TNFRSF1A

0.00E + 00

rs10849448

2.35E-35

   

NFKB1

9.08E-14

rs230523

4.54E-14

   

MAPK3

3.78E-06

rs12931792

4.06E-08

   

MAP2K2

4.75E-04

rs350906

5.34E-07

   

MYC

1.13E-03

rs13279820

1.44E-06

   

TRAF2

1.21E-02

rs17250694

1.56E-05

   

MADD

3.01E-02

rs2856661

3.76E-05

   

CTSD

3.13E-02

rs7929314

3.17E-05

   

CASP8

3.15E-02

rs190209406

3.72E-05

Glucocorticoid receptor regulatory network

5.00E-04

9.93E-03

NFKB1

9.08E-14

rs230523

4.54E-14

   

MAPK3

3.78E-06

rs12931792

4.06E-08

   

NCOA2

9.50E-04

rs1481046

5.65E-07

   

SELE

1.66E-03

rs6691453

5.38E-07

   

BGLAP

1.94E-03

rs2075165

2.52E-06

   

IL6

9.25E-03

rs57561814

7.45E-06

   

MAPK11

1.20E-02

rs4076566

1.23E-05

   

SMARCA4

1.41E-02

rs9797720

1.58E-05

   

SPI1

2.48E-02

rs11604680

3.38E-05

   

FKBP5

3.06E-02

rs74853132

1.68E-05

   

ICAM1

3.12E-02

rs74956615

4.07E-05

   

PCK2

3.34E-02

14:24604399:AAC_A

5.33E-05

  1. CI confidence interval, FDR false discovery rate, GWAS genome-wide association study, HLA human leukocyte antigen, MAGENTA Meta-Analysis Gene-set Enrichment of variaNT Associations, NA not applicable, OR odds ratio, SNP single-nucleotide polymorphism, UTI urinary tract infection
  2. The most significant pathway (gene sets) with a gene set enrichment FDR < 0.01 are presented
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